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(-) Description

Title :  STRUCTURE OF TT368 PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomic Initiative (Rsgi)
Date :  30 Aug 04  (Deposition) - 30 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydroxyisobutyrate, Nadp, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, N. Ohshima, K. Takio, I. Shiromizu, C. Kuroishi, N. Okazaki, S. Kuramitsu, S. Yokoyama, M. Miyano, N. Kunishima
Crystal Structure Of Novel Nadp-Dependent 3-Hydroxyisobutyrate Dehydrogenase From Thermus Thermophilu Hb8
J. Mol. Biol. V. 352 905 2005
PubMed-ID: 16126223  |  Reference-DOI: 10.1016/J.JMB.2005.07.068

(-) Compounds

Molecule 1 - 3-HYDROXYISOBUTYRATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:117 , GLY A:118 , GLY A:119 , LYS A:165 , ASN A:169 , NDP A:1301 , HOH A:1428 , SER B:204BINDING SITE FOR RESIDUE SO4 A 1305
2AC2SOFTWARESER A:204 , SER B:117 , GLY B:118 , GLY B:119 , LYS B:165 , ASN B:169 , NDP B:1302 , HOH B:1321 , HOH B:1446BINDING SITE FOR RESIDUE SO4 B 1306
3AC3SOFTWARESER C:117 , GLY C:118 , GLY C:119 , LYS C:165 , ASN C:169 , NDP C:1303 , HOH C:1362 , HOH C:1375 , SER D:204BINDING SITE FOR RESIDUE SO4 C 1307
4AC4SOFTWARESER D:117 , GLY D:118 , GLY D:119 , LYS D:165 , NDP D:1304 , HOH D:1395 , HOH D:1494BINDING SITE FOR RESIDUE SO4 D 1308
5AC5SOFTWAREGLY A:8 , LEU A:9 , GLY A:10 , ALA A:11 , MET A:12 , ASN A:30 , ARG A:31 , THR A:32 , LYS A:35 , CYS A:62 , LEU A:63 , PRO A:64 , GLU A:68 , GLU A:71 , THR A:90 , SER A:91 , VAL A:116 , GLY A:119 , LYS A:165 , THR A:226 , PHE A:227 , LYS A:234 , SO4 A:1305 , HOH A:1306 , HOH A:1307 , HOH A:1310 , HOH A:1314 , HOH A:1348 , HOH A:1354 , HOH A:1356 , HOH A:1386 , HOH A:1456 , HOH A:1460BINDING SITE FOR RESIDUE NDP A 1301
6AC6SOFTWAREGLY C:8 , LEU C:9 , GLY C:10 , ALA C:11 , MET C:12 , ASN C:30 , ARG C:31 , THR C:32 , CYS C:62 , LEU C:63 , PRO C:64 , GLU C:68 , GLU C:71 , SER C:91 , VAL C:116 , GLY C:119 , THR C:226 , PHE C:227 , LYS C:234 , SO4 C:1307 , HOH C:1312 , HOH C:1315 , HOH C:1327 , HOH C:1329 , HOH C:1332 , HOH C:1355 , HOH C:1400 , HOH C:1402 , HOH C:1413 , HOH C:1447 , HOH C:1464 , ARG D:105BINDING SITE FOR RESIDUE NDP C 1303
7AC7SOFTWARELEU D:9 , GLY D:10 , ALA D:11 , MET D:12 , ASN D:30 , ARG D:31 , THR D:32 , CYS D:62 , LEU D:63 , PRO D:64 , GLU D:68 , THR D:90 , SER D:91 , VAL D:116 , LYS D:165 , LYS D:234 , SO4 D:1308 , HOH D:1330 , HOH D:1345 , HOH D:1351 , HOH D:1360 , HOH D:1395 , HOH D:1465 , HOH D:1476 , HOH D:1484BINDING SITE FOR RESIDUE NDP D 1304
8AC8SOFTWAREGLY B:8 , LEU B:9 , GLY B:10 , ALA B:11 , MET B:12 , ASN B:30 , ARG B:31 , THR B:32 , CYS B:62 , LEU B:63 , PRO B:64 , GLU B:68 , GLU B:71 , THR B:90 , SER B:91 , VAL B:116 , GLY B:119 , THR B:226 , PHE B:227 , LYS B:234 , SO4 B:1306 , HOH B:1317 , HOH B:1324 , HOH B:1326 , HOH B:1330 , HOH B:1351 , HOH B:1355 , HOH B:1378BINDING SITE FOR RESIDUE NDP B 1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WP4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WP4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WP4)

(-) Exons   (0, 0)

(no "Exon" information available for 1WP4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:288
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
         Q5SLQ6_THET8     2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains d1wp4a2 A:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d1wp4a1 A:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 1wp4A01 A:2-157 NAD(P)-binding Rossmann-like Domain                                                                                                         1wp4A02 A:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhh...eeee...hhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhh...eeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wp4 A   2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
         Q5SLQ6_THET8     2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains d1wp4b2 B:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d1wp4b1 B:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 1wp4B01 B:2-157 NAD(P)-binding Rossmann-like Domain                                                                                                         1wp4B02 B:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhh...eeee..hhhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh...eeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wp4 B   2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        


Chain C from PDB  Type:PROTEIN  Length:289
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         
         Q5SLQ6_THET8     1 MEKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains -d1wp4c2 C:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d1wp4c1 C:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 1wp4C01 C:1-157 NAD(P)-binding Rossmann-like Domain                                                                                                          1wp4C02 C:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhh.eeee...hhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh.eeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wp4 C   1 MEKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         


Chain D from PDB  Type:PROTEIN  Length:289
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         
         Q5SLQ6_THET8     1 MEKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains -d1wp4d2 D:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d1wp4d1 D:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 1wp4D01 D:1-157 NAD(P)-binding Rossmann-like Domain                                                                                                          1wp4D02 D:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
           Pfam domains (1) NAD_binding_2-1wp4D01 D:1-157                                                                                                                                ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) NAD_binding_2-1wp4D02 D:1-157                                                                                                                                ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) NAD_binding_2-1wp4D03 D:1-157                                                                                                                                ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) NAD_binding_2-1wp4D04 D:1-157                                                                                                                                ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author ...eeee....hhhhhhhhhhhhh.eeee..hhhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wp4 D   1 MEKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SLQ6_THET8 | Q5SLQ6)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  1wp4
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  Q5SLQ6_THET8 | Q5SLQ6
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  1.1.1.31
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5SLQ6_THET8 | Q5SLQ6: 2cvz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WP4)